@include "_basic_sc_rna_counter_stages.mro"

call SUMMARIZE_READ_REPORTS(
    extract_reads_summary = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/join-udfa1937451/files/summary.json",
    barcode_counts = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/join-udfa1937451/files/barcode_counts.json",
    feature_counts = "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/join-udfa1937451/files/feature_counts.json",
    gem_groups = [
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1,
        1
    ],
    library_types = [
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression",
        "Gene Expression"
    ],
    library_ids = [
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0",
        "0"
    ],
    read_groups = [
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1",
        "tdtomato_run2:0:1:HJ5NCBGXB:1"
    ],
    align = {
        "aligner": "star",
        "high_conf_mapq": 255
    },
    bam_comments = [
        "10x_bam_to_fastq:I1(BC:QT)",
        "10x_bam_to_fastq:R1(CR:CY,UR:UY)",
        "10x_bam_to_fastq:R2(SEQ:QUAL)"
    ],
    read1s = [
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk16-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk17-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk18-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk19-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk20-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk21-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk22-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk23-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk24-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk25-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk26-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk27-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk28-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk29-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk30-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk31-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk32-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk33-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk34-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk35-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk36-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk37-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk38-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk39-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk40-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk41-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk42-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk43-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk44-udfa1937459/files/reads.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk45-udfa1937459/files/reads.fastq/1.fastq.lz4"
    ],
    read2s = [],
    tags = [
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk00-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk01-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk02-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk03-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk04-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk05-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk06-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk07-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk08-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk09-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk10-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk11-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk12-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk13-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk14-udfa1937459/files/tags.fastq/1.fastq.lz4",
        "/ufrc/ewang/lancetdenes/libLTD/tdtomato_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/EXTRACT_READS/fork0/chnk15-udfa1937459/files/tags.fastq/1.fastq.lz4",
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    ],
    retain_fastqs = false,
    chemistry_def = {
        "si_read_offset": 0,
        "strandedness": "+",
        "umi_read_offset": 16,
        "barcode_read_type": "R1",
        "umi_read_type": "R1",
        "barcode_read_length": 16,
        "rna_read_type": "R2",
        "barcode_whitelist": "3M-february-2018",
        "si_read_type": "I1",
        "rna_read_length": null,
        "description": "Single Cell 3' v3",
        "rna_read_offset": 0,
        "barcode_read_offset": 0,
        "rna_read2_type": null,
        "endedness": "three_prime",
        "name": "SC3Pv3",
        "umi_read_length": 12,
        "si_read_length": null,
        "read_type_to_bcl2fastq_filename": {
            "I1": "I1",
            "I2": null,
            "R1": "R1",
            "R2": "R2"
        },
        "rna_read2_length": null,
        "rna_read2_offset": 0,
        "read_type_to_bcl_processor_filename": {
            "I1": "I1",
            "I2": "I2",
            "R1": "RA",
            "R2": null
        }
    },
)